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<FONT color="green">001</FONT>    /*<a name="line.1"></a>
<FONT color="green">002</FONT>     * Licensed to the Apache Software Foundation (ASF) under one or more<a name="line.2"></a>
<FONT color="green">003</FONT>     * contributor license agreements.  See the NOTICE file distributed with<a name="line.3"></a>
<FONT color="green">004</FONT>     * this work for additional information regarding copyright ownership.<a name="line.4"></a>
<FONT color="green">005</FONT>     * The ASF licenses this file to You under the Apache License, Version 2.0<a name="line.5"></a>
<FONT color="green">006</FONT>     * (the "License"); you may not use this file except in compliance with<a name="line.6"></a>
<FONT color="green">007</FONT>     * the License.  You may obtain a copy of the License at<a name="line.7"></a>
<FONT color="green">008</FONT>     *<a name="line.8"></a>
<FONT color="green">009</FONT>     *      http://www.apache.org/licenses/LICENSE-2.0<a name="line.9"></a>
<FONT color="green">010</FONT>     *<a name="line.10"></a>
<FONT color="green">011</FONT>     * Unless required by applicable law or agreed to in writing, software<a name="line.11"></a>
<FONT color="green">012</FONT>     * distributed under the License is distributed on an "AS IS" BASIS,<a name="line.12"></a>
<FONT color="green">013</FONT>     * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.<a name="line.13"></a>
<FONT color="green">014</FONT>     * See the License for the specific language governing permissions and<a name="line.14"></a>
<FONT color="green">015</FONT>     * limitations under the License.<a name="line.15"></a>
<FONT color="green">016</FONT>     */<a name="line.16"></a>
<FONT color="green">017</FONT>    package org.apache.commons.math.genetics;<a name="line.17"></a>
<FONT color="green">018</FONT>    <a name="line.18"></a>
<FONT color="green">019</FONT>    import java.util.ArrayList;<a name="line.19"></a>
<FONT color="green">020</FONT>    import java.util.Arrays;<a name="line.20"></a>
<FONT color="green">021</FONT>    import java.util.Collections;<a name="line.21"></a>
<FONT color="green">022</FONT>    import java.util.Comparator;<a name="line.22"></a>
<FONT color="green">023</FONT>    import java.util.List;<a name="line.23"></a>
<FONT color="green">024</FONT>    <a name="line.24"></a>
<FONT color="green">025</FONT>    /**<a name="line.25"></a>
<FONT color="green">026</FONT>     * &lt;p&gt;<a name="line.26"></a>
<FONT color="green">027</FONT>     * Random Key chromosome is used for permutation representation. It is a vector<a name="line.27"></a>
<FONT color="green">028</FONT>     * of a fixed length of real numbers in [0,1] interval. The index of the i-th<a name="line.28"></a>
<FONT color="green">029</FONT>     * smallest value in the vector represents an i-th member of the permutation.<a name="line.29"></a>
<FONT color="green">030</FONT>     * &lt;/p&gt;<a name="line.30"></a>
<FONT color="green">031</FONT>     * <a name="line.31"></a>
<FONT color="green">032</FONT>     * &lt;p&gt;<a name="line.32"></a>
<FONT color="green">033</FONT>     * For example, the random key [0.2, 0.3, 0.8, 0.1] corresponds to the<a name="line.33"></a>
<FONT color="green">034</FONT>     * permutation of indices (3,0,1,2). If the original (unpermuted) sequence would<a name="line.34"></a>
<FONT color="green">035</FONT>     * be (a,b,c,d), this would mean the sequence (d,a,b,c).<a name="line.35"></a>
<FONT color="green">036</FONT>     * &lt;/p&gt;<a name="line.36"></a>
<FONT color="green">037</FONT>     * <a name="line.37"></a>
<FONT color="green">038</FONT>     * &lt;p&gt;<a name="line.38"></a>
<FONT color="green">039</FONT>     * With this representation, common operators like n-point crossover can be<a name="line.39"></a>
<FONT color="green">040</FONT>     * used, because any such chromosome represents a valid permutation.<a name="line.40"></a>
<FONT color="green">041</FONT>     * &lt;/p&gt;<a name="line.41"></a>
<FONT color="green">042</FONT>     * <a name="line.42"></a>
<FONT color="green">043</FONT>     * &lt;p&gt;<a name="line.43"></a>
<FONT color="green">044</FONT>     * Since the chromosome (and thus its arrayRepresentation) is immutable, the<a name="line.44"></a>
<FONT color="green">045</FONT>     * array representation is sorted only once in the constructor.<a name="line.45"></a>
<FONT color="green">046</FONT>     * &lt;/p&gt;<a name="line.46"></a>
<FONT color="green">047</FONT>     * <a name="line.47"></a>
<FONT color="green">048</FONT>     * &lt;p&gt;<a name="line.48"></a>
<FONT color="green">049</FONT>     * For details, see:<a name="line.49"></a>
<FONT color="green">050</FONT>     * &lt;ul&gt;<a name="line.50"></a>
<FONT color="green">051</FONT>     * &lt;li&gt;Bean, J.C.: Genetic algorithms and random keys for sequencing and<a name="line.51"></a>
<FONT color="green">052</FONT>     * optimization. ORSA Journal on Computing 6 (1994) 154–160&lt;/li&gt;<a name="line.52"></a>
<FONT color="green">053</FONT>     * &lt;li&gt;Rothlauf, F.: Representations for Genetic and Evolutionary Algorithms.<a name="line.53"></a>
<FONT color="green">054</FONT>     * Volume 104 of Studies in Fuzziness and Soft Computing. Physica-Verlag,<a name="line.54"></a>
<FONT color="green">055</FONT>     * Heidelberg (2002)&lt;/li&gt;<a name="line.55"></a>
<FONT color="green">056</FONT>     * &lt;/ul&gt;<a name="line.56"></a>
<FONT color="green">057</FONT>     * &lt;/p&gt;<a name="line.57"></a>
<FONT color="green">058</FONT>     * <a name="line.58"></a>
<FONT color="green">059</FONT>     * @param &lt;T&gt;<a name="line.59"></a>
<FONT color="green">060</FONT>     *            type of the permuted objects<a name="line.60"></a>
<FONT color="green">061</FONT>     * @since 2.0<a name="line.61"></a>
<FONT color="green">062</FONT>     * @version $Revision: 800113 $ $Date: 2009-08-02 13:23:54 -0400 (Sun, 02 Aug 2009) $<a name="line.62"></a>
<FONT color="green">063</FONT>     */<a name="line.63"></a>
<FONT color="green">064</FONT>    public abstract class RandomKey&lt;T&gt; extends AbstractListChromosome&lt;Double&gt; implements PermutationChromosome&lt;T&gt; {<a name="line.64"></a>
<FONT color="green">065</FONT>        <a name="line.65"></a>
<FONT color="green">066</FONT>        /**<a name="line.66"></a>
<FONT color="green">067</FONT>         * Cache of sorted representation (unmodifiable).<a name="line.67"></a>
<FONT color="green">068</FONT>         */<a name="line.68"></a>
<FONT color="green">069</FONT>        private final List&lt;Double&gt; sortedRepresentation;<a name="line.69"></a>
<FONT color="green">070</FONT>        <a name="line.70"></a>
<FONT color="green">071</FONT>        /**<a name="line.71"></a>
<FONT color="green">072</FONT>         * Base sequence [0,1,...,n-1], permuted accorting to the representation (unmodifiable).<a name="line.72"></a>
<FONT color="green">073</FONT>         */<a name="line.73"></a>
<FONT color="green">074</FONT>        private final List&lt;Integer&gt; baseSeqPermutation;<a name="line.74"></a>
<FONT color="green">075</FONT>        <a name="line.75"></a>
<FONT color="green">076</FONT>        /**<a name="line.76"></a>
<FONT color="green">077</FONT>         * Constructor.<a name="line.77"></a>
<FONT color="green">078</FONT>         * <a name="line.78"></a>
<FONT color="green">079</FONT>         * @param representation list of [0,1] values representing the permutation<a name="line.79"></a>
<FONT color="green">080</FONT>         */<a name="line.80"></a>
<FONT color="green">081</FONT>        public RandomKey(List&lt;Double&gt; representation) {<a name="line.81"></a>
<FONT color="green">082</FONT>            super(representation);<a name="line.82"></a>
<FONT color="green">083</FONT>            // store the sorted representation<a name="line.83"></a>
<FONT color="green">084</FONT>            List&lt;Double&gt; sortedRepr = new ArrayList&lt;Double&gt; (getRepresentation());<a name="line.84"></a>
<FONT color="green">085</FONT>            Collections.sort(sortedRepr);<a name="line.85"></a>
<FONT color="green">086</FONT>            sortedRepresentation = Collections.unmodifiableList(sortedRepr);<a name="line.86"></a>
<FONT color="green">087</FONT>            // store the permutation of [0,1,...,n-1] list for toString() and isSame() methods<a name="line.87"></a>
<FONT color="green">088</FONT>            baseSeqPermutation = Collections.unmodifiableList(<a name="line.88"></a>
<FONT color="green">089</FONT>                decodeGeneric(baseSequence(getLength()), getRepresentation(), sortedRepresentation)<a name="line.89"></a>
<FONT color="green">090</FONT>            );<a name="line.90"></a>
<FONT color="green">091</FONT>        }<a name="line.91"></a>
<FONT color="green">092</FONT>        <a name="line.92"></a>
<FONT color="green">093</FONT>        /**<a name="line.93"></a>
<FONT color="green">094</FONT>         * Constructor.<a name="line.94"></a>
<FONT color="green">095</FONT>         * <a name="line.95"></a>
<FONT color="green">096</FONT>         * @param representation array of [0,1] values representing the permutation<a name="line.96"></a>
<FONT color="green">097</FONT>         */<a name="line.97"></a>
<FONT color="green">098</FONT>        public RandomKey(Double[] representation) {<a name="line.98"></a>
<FONT color="green">099</FONT>            this(Arrays.asList(representation));<a name="line.99"></a>
<FONT color="green">100</FONT>        }<a name="line.100"></a>
<FONT color="green">101</FONT>    <a name="line.101"></a>
<FONT color="green">102</FONT>        /**<a name="line.102"></a>
<FONT color="green">103</FONT>         * {@inheritDoc}<a name="line.103"></a>
<FONT color="green">104</FONT>         */<a name="line.104"></a>
<FONT color="green">105</FONT>        public List&lt;T&gt; decode(List&lt;T&gt; sequence) {<a name="line.105"></a>
<FONT color="green">106</FONT>            return decodeGeneric(sequence, getRepresentation(), sortedRepresentation);<a name="line.106"></a>
<FONT color="green">107</FONT>        }<a name="line.107"></a>
<FONT color="green">108</FONT>    <a name="line.108"></a>
<FONT color="green">109</FONT>        /**<a name="line.109"></a>
<FONT color="green">110</FONT>         * Decodes a permutation represented by &lt;code&gt;representation&lt;/code&gt; and<a name="line.110"></a>
<FONT color="green">111</FONT>         * returns a (generic) list with the permuted values.<a name="line.111"></a>
<FONT color="green">112</FONT>         * <a name="line.112"></a>
<FONT color="green">113</FONT>         * @param &lt;S&gt; generic type of the sequence values<a name="line.113"></a>
<FONT color="green">114</FONT>         * @param sequence the unpermuted sequence<a name="line.114"></a>
<FONT color="green">115</FONT>         * @param representation representation of the permutation ([0,1] vector)<a name="line.115"></a>
<FONT color="green">116</FONT>         * @param sortedRepr sorted &lt;code&gt;representation&lt;/code&gt;<a name="line.116"></a>
<FONT color="green">117</FONT>         * @return list with the sequence values permuted according to the representation<a name="line.117"></a>
<FONT color="green">118</FONT>         */<a name="line.118"></a>
<FONT color="green">119</FONT>        private static &lt;S&gt; List&lt;S&gt; decodeGeneric(List&lt;S&gt; sequence, List&lt;Double&gt; representation, List&lt;Double&gt; sortedRepr) {<a name="line.119"></a>
<FONT color="green">120</FONT>            int l = sequence.size();<a name="line.120"></a>
<FONT color="green">121</FONT>            <a name="line.121"></a>
<FONT color="green">122</FONT>            if (representation.size() != l) {<a name="line.122"></a>
<FONT color="green">123</FONT>                throw new IllegalArgumentException(String.format("Length of sequence for decoding (%s) has to be equal to the length of the RandomKey (%s)", l, representation.size()));<a name="line.123"></a>
<FONT color="green">124</FONT>            }<a name="line.124"></a>
<FONT color="green">125</FONT>            if (representation.size() != sortedRepr.size()) {<a name="line.125"></a>
<FONT color="green">126</FONT>                throw new IllegalArgumentException(String.format("Representation and sortedRepr must have same sizes, %d != %d", representation.size(), sortedRepr.size()));<a name="line.126"></a>
<FONT color="green">127</FONT>            }<a name="line.127"></a>
<FONT color="green">128</FONT>            <a name="line.128"></a>
<FONT color="green">129</FONT>            List&lt;Double&gt; reprCopy = new ArrayList&lt;Double&gt; (representation);// do not modify the orig. representation<a name="line.129"></a>
<FONT color="green">130</FONT>            <a name="line.130"></a>
<FONT color="green">131</FONT>            // now find the indices in the original repr and use them for permuting<a name="line.131"></a>
<FONT color="green">132</FONT>            List&lt;S&gt; res = new ArrayList&lt;S&gt; (l);<a name="line.132"></a>
<FONT color="green">133</FONT>            for (int i=0; i&lt;l; i++) {<a name="line.133"></a>
<FONT color="green">134</FONT>                int index = reprCopy.indexOf(sortedRepr.get(i));<a name="line.134"></a>
<FONT color="green">135</FONT>                res.add(sequence.get(index));<a name="line.135"></a>
<FONT color="green">136</FONT>                reprCopy.set(index, null);<a name="line.136"></a>
<FONT color="green">137</FONT>            }<a name="line.137"></a>
<FONT color="green">138</FONT>            return res;<a name="line.138"></a>
<FONT color="green">139</FONT>        }<a name="line.139"></a>
<FONT color="green">140</FONT>    <a name="line.140"></a>
<FONT color="green">141</FONT>        /**<a name="line.141"></a>
<FONT color="green">142</FONT>         * Returns &lt;code&gt;true&lt;/code&gt; iff &lt;code&gt;another&lt;/code&gt; is a RandomKey and<a name="line.142"></a>
<FONT color="green">143</FONT>         * encodes the same permutation.<a name="line.143"></a>
<FONT color="green">144</FONT>         * <a name="line.144"></a>
<FONT color="green">145</FONT>         * @param another chromosome to compare<a name="line.145"></a>
<FONT color="green">146</FONT>         * @return true iff chromosomes encode the same permutation<a name="line.146"></a>
<FONT color="green">147</FONT>         */<a name="line.147"></a>
<FONT color="green">148</FONT>        @Override<a name="line.148"></a>
<FONT color="green">149</FONT>        protected boolean isSame(Chromosome another) {<a name="line.149"></a>
<FONT color="green">150</FONT>            // type check<a name="line.150"></a>
<FONT color="green">151</FONT>            if (! (another instanceof RandomKey&lt;?&gt;))<a name="line.151"></a>
<FONT color="green">152</FONT>                return false;<a name="line.152"></a>
<FONT color="green">153</FONT>            RandomKey&lt;?&gt; anotherRk = (RandomKey&lt;?&gt;) another;<a name="line.153"></a>
<FONT color="green">154</FONT>            // size check<a name="line.154"></a>
<FONT color="green">155</FONT>            if (getLength() != anotherRk.getLength())<a name="line.155"></a>
<FONT color="green">156</FONT>                return false;<a name="line.156"></a>
<FONT color="green">157</FONT>            <a name="line.157"></a>
<FONT color="green">158</FONT>            // two different representations can still encode the same permutation<a name="line.158"></a>
<FONT color="green">159</FONT>            // the ordering is what counts<a name="line.159"></a>
<FONT color="green">160</FONT>            List&lt;Integer&gt; thisPerm = this.baseSeqPermutation;<a name="line.160"></a>
<FONT color="green">161</FONT>            List&lt;Integer&gt; anotherPerm = anotherRk.baseSeqPermutation;<a name="line.161"></a>
<FONT color="green">162</FONT>            <a name="line.162"></a>
<FONT color="green">163</FONT>            for (int i=0; i&lt;getLength(); i++) {<a name="line.163"></a>
<FONT color="green">164</FONT>                if (thisPerm.get(i) != anotherPerm.get(i))<a name="line.164"></a>
<FONT color="green">165</FONT>                    return false;<a name="line.165"></a>
<FONT color="green">166</FONT>            }<a name="line.166"></a>
<FONT color="green">167</FONT>            // the permutations are the same<a name="line.167"></a>
<FONT color="green">168</FONT>            return true;<a name="line.168"></a>
<FONT color="green">169</FONT>        }<a name="line.169"></a>
<FONT color="green">170</FONT>        <a name="line.170"></a>
<FONT color="green">171</FONT>        /**<a name="line.171"></a>
<FONT color="green">172</FONT>         * {@inheritDoc}<a name="line.172"></a>
<FONT color="green">173</FONT>         */<a name="line.173"></a>
<FONT color="green">174</FONT>        @Override    <a name="line.174"></a>
<FONT color="green">175</FONT>        protected void checkValidity(java.util.List&lt;Double&gt; representation) throws InvalidRepresentationException {<a name="line.175"></a>
<FONT color="green">176</FONT>            for (double val : representation) {<a name="line.176"></a>
<FONT color="green">177</FONT>                if (val &lt; 0 || val &gt; 1) {<a name="line.177"></a>
<FONT color="green">178</FONT>                    throw new InvalidRepresentationException("Values of representation must be in [0,1] interval");<a name="line.178"></a>
<FONT color="green">179</FONT>                }<a name="line.179"></a>
<FONT color="green">180</FONT>            }<a name="line.180"></a>
<FONT color="green">181</FONT>        }<a name="line.181"></a>
<FONT color="green">182</FONT>        <a name="line.182"></a>
<FONT color="green">183</FONT>    <a name="line.183"></a>
<FONT color="green">184</FONT>        /**<a name="line.184"></a>
<FONT color="green">185</FONT>         * Generates a representation corresponding to a random permutation of<a name="line.185"></a>
<FONT color="green">186</FONT>         * length l which can be passed to the RandomKey constructor.<a name="line.186"></a>
<FONT color="green">187</FONT>         * <a name="line.187"></a>
<FONT color="green">188</FONT>         * @param l<a name="line.188"></a>
<FONT color="green">189</FONT>         *            length of the permutation<a name="line.189"></a>
<FONT color="green">190</FONT>         * @return representation of a random permutation<a name="line.190"></a>
<FONT color="green">191</FONT>         */<a name="line.191"></a>
<FONT color="green">192</FONT>        public static final List&lt;Double&gt; randomPermutation(int l) {<a name="line.192"></a>
<FONT color="green">193</FONT>            List&lt;Double&gt; repr = new ArrayList&lt;Double&gt;(l);<a name="line.193"></a>
<FONT color="green">194</FONT>            for (int i=0; i&lt;l; i++) {<a name="line.194"></a>
<FONT color="green">195</FONT>                repr.add(GeneticAlgorithm.getRandomGenerator().nextDouble());<a name="line.195"></a>
<FONT color="green">196</FONT>            }<a name="line.196"></a>
<FONT color="green">197</FONT>            return repr;<a name="line.197"></a>
<FONT color="green">198</FONT>        }<a name="line.198"></a>
<FONT color="green">199</FONT>    <a name="line.199"></a>
<FONT color="green">200</FONT>        /**<a name="line.200"></a>
<FONT color="green">201</FONT>         * Generates a representation corresponding to an identity permutation of<a name="line.201"></a>
<FONT color="green">202</FONT>         * length l which can be passed to the RandomKey constructor.<a name="line.202"></a>
<FONT color="green">203</FONT>         * <a name="line.203"></a>
<FONT color="green">204</FONT>         * @param l<a name="line.204"></a>
<FONT color="green">205</FONT>         *            length of the permutation<a name="line.205"></a>
<FONT color="green">206</FONT>         * @return representation of an identity permutation<a name="line.206"></a>
<FONT color="green">207</FONT>         */<a name="line.207"></a>
<FONT color="green">208</FONT>        public static final List&lt;Double&gt; identityPermutation(int l) {<a name="line.208"></a>
<FONT color="green">209</FONT>            List&lt;Double&gt; repr = new ArrayList&lt;Double&gt;(l);<a name="line.209"></a>
<FONT color="green">210</FONT>            for (int i=0; i&lt;l; i++) {<a name="line.210"></a>
<FONT color="green">211</FONT>                repr.add((double)i/l);<a name="line.211"></a>
<FONT color="green">212</FONT>            }<a name="line.212"></a>
<FONT color="green">213</FONT>            return repr;<a name="line.213"></a>
<FONT color="green">214</FONT>        }<a name="line.214"></a>
<FONT color="green">215</FONT>    <a name="line.215"></a>
<FONT color="green">216</FONT>        /**<a name="line.216"></a>
<FONT color="green">217</FONT>         * Generates a representation of a permutation corresponding to the<a name="line.217"></a>
<FONT color="green">218</FONT>         * &lt;code&gt;data&lt;/code&gt; sorted by &lt;code&gt;comparator&lt;/code&gt;. The<a name="line.218"></a>
<FONT color="green">219</FONT>         * &lt;code&gt;data&lt;/code&gt; is not modified during the process.<a name="line.219"></a>
<FONT color="green">220</FONT>         * <a name="line.220"></a>
<FONT color="green">221</FONT>         * This is useful if you want to inject some permutations to the initial<a name="line.221"></a>
<FONT color="green">222</FONT>         * population.<a name="line.222"></a>
<FONT color="green">223</FONT>         * <a name="line.223"></a>
<FONT color="green">224</FONT>         * @param &lt;S&gt; type of the data<a name="line.224"></a>
<FONT color="green">225</FONT>         * @param data list of data determining the order<a name="line.225"></a>
<FONT color="green">226</FONT>         * @param comparator how the data will be compared<a name="line.226"></a>
<FONT color="green">227</FONT>         * @return list representation of the permutation corresponding to the parameters<a name="line.227"></a>
<FONT color="green">228</FONT>         */<a name="line.228"></a>
<FONT color="green">229</FONT>        public static &lt;S&gt; List&lt;Double&gt; comparatorPermutation(List&lt;S&gt; data, Comparator&lt;S&gt; comparator) {<a name="line.229"></a>
<FONT color="green">230</FONT>            List&lt;S&gt; sortedData = new ArrayList&lt;S&gt; (data);<a name="line.230"></a>
<FONT color="green">231</FONT>            Collections.sort(sortedData, comparator);<a name="line.231"></a>
<FONT color="green">232</FONT>            <a name="line.232"></a>
<FONT color="green">233</FONT>            return inducedPermutation(data, sortedData);<a name="line.233"></a>
<FONT color="green">234</FONT>        }<a name="line.234"></a>
<FONT color="green">235</FONT>    <a name="line.235"></a>
<FONT color="green">236</FONT>        /**<a name="line.236"></a>
<FONT color="green">237</FONT>         * Generates a representation of a permutation corresponding to a<a name="line.237"></a>
<FONT color="green">238</FONT>         * permutation which yields &lt;code&gt;permutedData&lt;/code&gt; when applied to<a name="line.238"></a>
<FONT color="green">239</FONT>         * &lt;code&gt;originalData&lt;/code&gt;.<a name="line.239"></a>
<FONT color="green">240</FONT>         * <a name="line.240"></a>
<FONT color="green">241</FONT>         * This method can be viewed as an inverse to {@link #decode(List)}.<a name="line.241"></a>
<FONT color="green">242</FONT>         * <a name="line.242"></a>
<FONT color="green">243</FONT>         * @param &lt;S&gt; type of the data<a name="line.243"></a>
<FONT color="green">244</FONT>         * @param originalData the original, unpermuted data<a name="line.244"></a>
<FONT color="green">245</FONT>         * @param permutedData the data, somehow permuted<a name="line.245"></a>
<FONT color="green">246</FONT>         * @return representation of a permutation corresponding to the permutation &lt;code&gt;originalData -&gt; permutedData&lt;/code&gt;<a name="line.246"></a>
<FONT color="green">247</FONT>         * @throws IllegalArgumentException iff the &lt;code&gt;permutedData&lt;/code&gt; and &lt;code&gt;originalData&lt;/code&gt; contains different data <a name="line.247"></a>
<FONT color="green">248</FONT>         */<a name="line.248"></a>
<FONT color="green">249</FONT>        public static &lt;S&gt; List&lt;Double&gt; inducedPermutation(List&lt;S&gt; originalData, List&lt;S&gt; permutedData) throws IllegalArgumentException {<a name="line.249"></a>
<FONT color="green">250</FONT>            if (originalData.size() != permutedData.size()) {<a name="line.250"></a>
<FONT color="green">251</FONT>                throw new IllegalArgumentException("originalData and permutedData must have same length");<a name="line.251"></a>
<FONT color="green">252</FONT>            }<a name="line.252"></a>
<FONT color="green">253</FONT>            int l = originalData.size();<a name="line.253"></a>
<FONT color="green">254</FONT>            <a name="line.254"></a>
<FONT color="green">255</FONT>            List&lt;S&gt; origDataCopy = new ArrayList&lt;S&gt; (originalData);<a name="line.255"></a>
<FONT color="green">256</FONT>            <a name="line.256"></a>
<FONT color="green">257</FONT>            Double[] res = new Double[l];<a name="line.257"></a>
<FONT color="green">258</FONT>            for (int i=0; i&lt;l; i++) {<a name="line.258"></a>
<FONT color="green">259</FONT>                int index = origDataCopy.indexOf(permutedData.get(i));<a name="line.259"></a>
<FONT color="green">260</FONT>                if (index == -1) {<a name="line.260"></a>
<FONT color="green">261</FONT>                    throw new IllegalArgumentException("originalData and permutedData must contain the same objects.");<a name="line.261"></a>
<FONT color="green">262</FONT>                }<a name="line.262"></a>
<FONT color="green">263</FONT>                res[index] = (double) i / l;<a name="line.263"></a>
<FONT color="green">264</FONT>                origDataCopy.set(index, null);<a name="line.264"></a>
<FONT color="green">265</FONT>            }<a name="line.265"></a>
<FONT color="green">266</FONT>            return Arrays.asList(res);<a name="line.266"></a>
<FONT color="green">267</FONT>        }<a name="line.267"></a>
<FONT color="green">268</FONT>        <a name="line.268"></a>
<FONT color="green">269</FONT>        /**<a name="line.269"></a>
<FONT color="green">270</FONT>         * {@inheritDoc}<a name="line.270"></a>
<FONT color="green">271</FONT>         */<a name="line.271"></a>
<FONT color="green">272</FONT>        @Override<a name="line.272"></a>
<FONT color="green">273</FONT>        public String toString() {<a name="line.273"></a>
<FONT color="green">274</FONT>            return String.format("(f=%s pi=(%s))", getFitness(), baseSeqPermutation);<a name="line.274"></a>
<FONT color="green">275</FONT>        }<a name="line.275"></a>
<FONT color="green">276</FONT>    <a name="line.276"></a>
<FONT color="green">277</FONT>        /**<a name="line.277"></a>
<FONT color="green">278</FONT>         * Helper for constructor. Generates a list of natural numbers (0,1,...,l-1).<a name="line.278"></a>
<FONT color="green">279</FONT>         * <a name="line.279"></a>
<FONT color="green">280</FONT>         * @param l length of list to generate<a name="line.280"></a>
<FONT color="green">281</FONT>         * @return list of integers from 0 to l-1<a name="line.281"></a>
<FONT color="green">282</FONT>         */<a name="line.282"></a>
<FONT color="green">283</FONT>        private static List&lt;Integer&gt; baseSequence(int l) {<a name="line.283"></a>
<FONT color="green">284</FONT>            List&lt;Integer&gt; baseSequence = new ArrayList&lt;Integer&gt; (l);<a name="line.284"></a>
<FONT color="green">285</FONT>            for (int i=0; i&lt;l; i++) {<a name="line.285"></a>
<FONT color="green">286</FONT>                baseSequence.add(i);<a name="line.286"></a>
<FONT color="green">287</FONT>            }<a name="line.287"></a>
<FONT color="green">288</FONT>            return baseSequence;<a name="line.288"></a>
<FONT color="green">289</FONT>        }<a name="line.289"></a>
<FONT color="green">290</FONT>    }<a name="line.290"></a>




























































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